bulkrna-splicing

name	bulkrna-splicing
description	Alternative splicing analysis — PSI quantification, differential splicing event detection from rMATS/SUPPA2 output.
version	0.3.0
author	OmicsClaw
license	MIT
tags	["bulkrna","splicing","alternative-splicing","PSI","rMATS","SUPPA2"]
metadata	{"omicsclaw":{"domain":"bulkrna","emoji":"🧬","trigger_keywords":["alternative splicing","splicing analysis","PSI","rMATS","SUPPA2","exon skipping","differential splicing"],"allowed_extra_flags":["--dpsi-cutoff","--padj-cutoff"],"legacy_aliases":["bulk-splicing"],"saves_h5ad":false}}

Bulk RNA-seq Alternative Splicing Analysis

Alternative splicing quantification and differential splicing event detection. Accepts pre-computed splicing event tables (e.g. from rMATS or SUPPA2), computes PSI-based statistics, identifies significant differential splicing events, and produces publication-ready visualizations.

CLI Reference

python omicsclaw.py run bulkrna-splicing --demo
python omicsclaw.py run bulkrna-splicing --input <splicing_events.csv> --output <dir>
python bulkrna_splicing.py --input events.csv --output results/ --dpsi-cutoff 0.1 --padj-cutoff 0.05
python bulkrna_splicing.py --demo --output /tmp/splicing_demo

Why This Exists

• Without it: Researchers must manually parse rMATS/SUPPA2 output files, compute delta-PSI statistics, apply multiple-testing correction, and create splicing-specific visualizations across thousands of events.
• With it: A single Python command summarizes splicing events by type, identifies significant differential splicing, and produces volcano plots and event-type distributions ready for publication.
• Why OmicsClaw: Wraps standard alternative splicing analysis into the OmicsClaw reporting framework with consistent output structure, reproducibility scripts, and automatic demo data generation.

Algorithm / Methodology

Splicing Event Types

Abbreviation	Event Type	Description
SE	Skipped Exon	An exon is included or excluded from the transcript
A5SS	Alternative 5' Splice Site	Two or more 5' splice sites for the same exon
A3SS	Alternative 3' Splice Site	Two or more 3' splice sites for the same exon
MXE	Mutually Exclusive Exons	One of two exons is included, not both
RI	Retained Intron	An intron is retained in the mature transcript

PSI Quantification

Percent Spliced In (PSI) measures the fraction of transcripts that include a given exon or splice site:

PSI = inclusion_reads / (inclusion_reads + exclusion_reads)

Delta-PSI (dPSI) between conditions:

dPSI = PSI_treatment - PSI_control

Statistical Testing

• Per-event t-test: Welch's t-test on PSI replicates between conditions
• Multiple testing correction: Benjamini-Hochberg FDR
• Significance thresholds: |dPSI| > cutoff AND padj < cutoff

Upstream Tools

This skill operates on pre-computed splicing event tables produced by:

• rMATS (replicate Multivariate Analysis of Transcript Splicing) — detects differential alternative splicing from replicate RNA-seq data
• SUPPA2 — fast quantification of splicing events from transcript-level TPMs

Parameters

Parameter	Default	Description
--input	—	Path to splicing events CSV
--output	—	Output directory (required)
--demo	—	Run with synthetic demo data
--dpsi-cutoff	0.1	Absolute delta-PSI threshold for significance
--padj-cutoff	0.05	Adjusted p-value threshold for significance

Workflow

1. Load: Read a splicing events table (CSV with event_id, event_type, gene, psi_ctrl, psi_treat, delta_psi, pvalue, padj columns).
2. Summarize: Count events by type, compute overall statistics.
3. Filter: Identify significant differential splicing events by |dPSI| and adjusted p-value thresholds.
4. Visualize: Generate event type distribution (pie chart), delta-PSI histogram, and splicing volcano plot.
5. Report: Write markdown report, result.json, full and filtered event tables, and a reproducibility script.

Example Queries

• "Analyze alternative splicing events from my rMATS output"
• "Find significant differential splicing between conditions"
• "Show me the distribution of splicing event types"
• "Run splicing analysis with a delta-PSI cutoff of 0.15"

Output Structure

output_directory/
├── report.md
├── result.json
├── figures/
│   ├── event_type_distribution.png
│   ├── dpsi_distribution.png
│   └── volcano_splicing.png
├── tables/
│   ├── splicing_events.csv
│   └── significant_events.csv
└── reproducibility/
    └── commands.sh

Safety

• Local-first: All processing runs locally; no data is uploaded to external services.
• Disclaimer: Every report includes the standard OmicsClaw disclaimer.
• Audit trail: Parameters, thresholds, and input metadata are recorded in result.json.

Integration with Orchestrator

Trigger conditions:

• Automatically invoked when user intent matches alternative splicing analysis keywords.

Chaining partners:

• bulkrna-qc — Upstream: count matrix QC
• bulkrna-de — Parallel: gene-level differential expression to complement exon-level splicing
• bulkrna-enrichment — Downstream: pathway enrichment of genes with significant splicing changes

Version Compatibility

Reference examples tested with: scipy 1.11+, pandas 2.0+, numpy 1.24+, matplotlib 3.7+

Dependencies

Required: numpy, pandas, scipy, matplotlib

Citations

• rMATS — Shen et al., PNAS 2014
• SUPPA2 — Trincado et al., Genome Research 2018
• Benjamini-Hochberg — Benjamini & Hochberg, JRSSB 1995

Related Skills

• bulkrna-qc — Count matrix QC upstream
• bulkrna-de — Gene-level differential expression
• bulkrna-enrichment — Pathway enrichment of affected genes